[Bioperl-l] Bio::DB::Fasta check for ragged line widths

Lincoln Stein lstein at cshl.edu
Tue Apr 10 18:01:37 EDT 2007


I'm happy I didn't catch this thread until just now, but my preferred course
of action was to do exactly what Brian did and accept the patch.

Lincoln

On 4/10/07, Brian Osborne <bosborne11 at verizon.net> wrote:
>
> OK, applied.
>
>
> On 4/6/07 11:31 PM, "Don Gilbert" <gilbertd at cricket.bio.indiana.edu>
> wrote:
>
> >   +      $l3_len= $l2_len; $l2_len= $l_len; $l_len= length($_); # need
> to
> > check every line :(
> >   +      if(DIE_ON_MISSMATCHED_LINES &&
> >   +        $l3_len>0 && $l2_len>0 && $l3_len!=$l2_len) {
> >   +         my $fap= substr($_,0,20)."..";
> >   +         $self->throw("Each line of the fasta entry must be the same
> length
> > except the last.
> >   +  Line above #$. '$fap' is $l2_len != $l3_len chars.");
> >   +         }
>
>
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Lincoln D. Stein
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